345098
doi
10.5281/zenodo.345098
oai:zenodo.org:345098
Lavenier, Dominique
CNRS, GenScale
Gibrat, Jean-François
INRA, IFB
Dominguez del Angel, Victoria
CNRS, IFB, Elixir
Evaluation of genome assembly software based on long reads
Bouri, Laurent
CNRS, IFB
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Third-generation sequencing
Pacific Biosciences (PacBio)
Oxford nanopore MinION
De novo assembly
Genome
Bioinformatics
<p>During the last 30 years, Genomics has been revolutionized by the development of first- and second-generation sequencing (SGS) technologies, enabling the completion of many remarkable projects as the Human Genome Project, the 1000 Genomes Project and the Human Microbiome Project.<br>
In the last decade, SGS technologies based on massive parallel sequencing have dominated the market, thanks to their ability to produce enormous volumes of data cheaply. However, often genes and regions of interest are not completely or accurately assembled, complicating analyses or requiring additional cloning efforts for obtaining the correct sequences. The fundamental obstacle in SGS technologies for obtaining high quality genome assembly is the existence of repetitions in the sequences. A promising solution to this issue is the advent of Third-generation sequencing (TGS) technologies based on long read sequencing.</p>
<p>TGS technologies have been used to produce highly accurate <em>de novo </em>assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence diversity. They have also been applied to resequencing analyses, to create detailed maps of structural variations in many species. Also, these new technologies have been used to fill in many of the gaps in the human reference genome. In this report, we compare and evaluate several genome assembly software based on TSG technology. The experimentation has been performed on 4 reference genomes and the results evaluated with the QUAST software.</p>
Zenodo
2017-03-02
info:eu-repo/semantics/technicalDocumentation
780856
1579541719.32513
382699
md5:33ea1aaad2dcf45b2d948f556344825f
https://zenodo.org/records/345098/files/scientific_reports_assembly_long_reads(2).pdf
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